The End Of Cities
by summernw
Summary: The story starts after Valentines death. Up until that point, Clary has spent her whole life with Valentine an Sebastian in Idris, but instead of going into hiding with Sebastian, She is sent to live with the shadow hunters and to try to have a normal life. M because...well, you'll just have to see. :)
1. Prologue

**The End of Cities**

Prologue

This story starts after Valentine died. Clary's mother never left Valentine and she grew up there. It starts of sad but it turns up quickly.

The men led Clarissa by the hand out of the home she always knew. They asked her here name but she offered no response. As she left the big solid doors she would lean against and day dream her heart sank. And flew. The world was beautiful. The grass was green and she heard lovely birds. Her brother told her to not be afraid, to be strong. He said this would be good for her and to enjoy herself for the time being. He said he would be back for her soon enough.

The men put her on the back of a horse and took her away to the City of Glass. They put her in an auditorium like room where the people looked down on her with pure hate and fear. They asked her question she couldn't answer. They put a blade in her hands to force the answer out of her. They didn't stop until her hands bleed. She thought about answering them and what it would be like if she could.

A tall man walked out of a passage. His clock was the color of bone and his face mutilated. He turned to the council and without words told them that she was incapable of speech. She was so exhausted that the next exchange of words was lost. She caught something about finding people she knew, but the rest was a sea of incoherent sound. The man in the robe collected her in his arms and carried her through a portal that led to her next place of residence.


	2. Chapter 1: Remember Me

Chapter 1 : Remember Me

Clarissa woke up in a small plain room. It wasn't the way she'd always imagined leaving home would be. She laid still in her bed wondering where the cute singing birds were. She loved birds she always thought they were so pretty. Her minded drifted to looking thought the books father had brought home for her. She remembered how her brother would sit with her and read too.

Her mind became too active to just lay still. She popped out of bed and started searching her room for some paper. The room was completely sterile of it, so she thought it would be the best to look elsewhere.

She left the room for a long narrow hallway. She walked along it opening doors. All the rooms were the same blank with a large bed in the center. No real belonging to be found anywhere. She decided to turn down the next corridor. In her way was an extra, fluffy extra pissed off blue cat. It hissed and arched its back. Clarissa tried to side step it, but the cat lunged at her causing her to trip and fall with a thud.

The door across from her opened. A fair haired boy peered down at her.

"Umm… So you're Clarissa right. We met when we were little, remember," he helped he up, "My name's Jace."

Clarrisa nodded and smiled. He looked her momentarily confused. "Sorry, I forgot about the talking thing. Don't get worked up over it. I'm sure they'll figure a way round it. Let's go meet the others."

He walked her through the winding passages of the institute into the dining room were everyone was gathered.

There was a good five or so seconds of silence while everyone watched her. Jace cleared his throat. Mayrse slapped on her fake smile, "Hello, dear. Welcome to the New York Institute. You'll be staying her for the foreseen future. These are my children Alec and Isabelle. You've already met Jace."

Alec stood and shook her hand without any emotion. "Nice to meet you." He left the room without another word.

Isabelle got up next. She took her hand and looked her in the eye. "I would say nice to meet you, but it is an honest punishment to be in the same room with you. I'm truly sorry for you." She flipped her off, "Goodnight liarer."


	3. Chapter 2: I Denied

Chapter 2: I Denied

Clarissa smiled. She'd be laughing if she could make a sound. '_Weak_'.

Jace pointed to her and looked at Mayrse. "I like this one." She wasn't really paying attention to him. She walked over to Clarissa and led her to a chair.

"Now, I know you've never been out of that house before and the clave can be very frightening, but if there is anything you know about what your brother is doing or where the missing people are, you need to tell me." She handed her a pen and paper. "My son, Max, was taken. Tell me where he is."

Clarissa picked up the pen slowly. Mayrse as gently, "Can you write?" Clarissa wrote in almost a style of calligraphy. "Yes_._"

"Do you know where the missing are?"

"He hasn't told me."

"What has he told you?"

"Your questions are irrelevant. The council you put me in front of already asked me this. Did you think they really wouldn't give me a pen? I told you he never told me what he's doing. He said to wait and to be unafraid. Please I don't want to hear more of how you will kill my only family. Why do you people forget that he's still my brother?"Clarrisa's eyes were pleading.

"I understand. Have a good after noon Ms. Morgenstern." She sighed deeply. "Why don't you take her outside, Jace?"

They walked out of the institute in silence. On the street cars bustled by and people scurried to their destinations. It was started to get dark and all the light form the city were beginning to sparkle.

Jace brought her to a little building with the name Taki's sprawled across the front in red letters. "This is where anyone that's a part of the shadow world comes to eat," Jace explained. "You know what that is, right?"

Clarissa nodded. They sat down at an empty booth. Soon a waitress with multi-colored skin came by. "Jace! Nice to see you. Want the same thing as always?"

"Umm, yeah could you do me a favor? My friend her doesn't really talk can I get some paper or napkins."

"Sure thing, but I really don't see what the clave is doing integrating a little mundane."

"She's a Nephilim. She just doesn't have any marks yet." The waitress winked and a few awkwardly silent moments later returned with a little notepad and a pen.

Clarrisa took the pen. "How'd you get all the way out here?"

Jace sighed. "Valentine stopped coming, so eventually I just left home. I didn't know he was Valentine at the time, so yeah. The clave put me here at random."

"You were the first person I ever saw outside of the family. I tried to go back to see you. Sebastian caught me though." Clarrisa explained.

"Did put that spell on you to stop you from coming to talk to me?" Jace felt guilt build in his chest.

Clarrisa shook her head. "Valentine had the spell put on me. Sebastian sat me down an explained to me why I couldn't go," she took a slow breath. "I miss him. He is a bashful little hellion to everyone, but me. He was always so nice to me."

"Did you think he'd be capable of this," Jace said

"Of course, I'm not blind," She wrote.

"Why didn't he take you with him?" Clarrisa tapped the pen on the paper, but didn't write. "Do you agree with what he's doing?"

"No. It's why I denied him."


	4. Chapter 3 : Stronger Than You Thought

Chapter 3: Stonger than you thought

"Wow," Jace laughed, "So how does he handle rejection?"

"Like an over privileged demonic five year old." Clarrisa smiled brightly.

"Hey let's skip the food. I think Alec and Isabelle are planning or deaths right now."

Clarrisa looed quizzically and wrote, "Why you?"

"Because I knew you before all this and for some reason they thin I knew Sebastian by extension." He explained, "Also they don't like me for not complaining about having you here. You seemed nice as a kid."

Clarrisa looked down to write her reply, but she'd turned the paper and wrote in between messages so much that it was all unintelligible. She wrote on her hand and showed him with a smile, "Let's go back then."

They walked out of the restraint and down the street for a while until she stopped him. She glared at him and pointed to the cars. "Sorry, I thought we'd get home faster by subway. It's impossible to get a taxi at this time." She rolled her pretty green eyes.

Ace started to walk them through a less densely populate area where the buildings open up to form black alley ways. Clarrisa noted out of the corner of her eye someone coming out of one of these allies while Jace was talking. She wasn't really listening. The thing saw seemed fairly quick. She heard a foot step just a little too close. She turned on her heels and threw a knife. A shrill cry went up into the night. Jace swear and took out a seraph blade but the demon was already dead. Clarrisa walked over to the demon and crouched down. She stared down at it until she saw that she wanted. She moved her hand to grab it, but Jace pulled her up. "Hey, you probably shouldn't do that." She shh-ed him. She crouched down and picked up her knife.

"Where did you find that?" Jace grabbed her wrist and took the knife. She stared at him with blatant irritation. Jace sighed and lowered the knife, "Sorry, you can't speak. Almost forgot."

Clarrisa smiled brightly. She had a very nice idea. In a smooth, easy motion she snatched the knife out of Jace's hand and took off running down the street. She managed to lose him in a fairly short amount of time. She was mildly disappointed. Maybe she missed his company or maybe because she thought she was faster.

Jace returned to the institute having given up on finding Clarrisa. He went to Alec's room to ask to help him search for her. He said something along the lines of not want Isabelle that angry at him right now. Jace sucked up his pride and asked Isabelle thinking if he could get her, he would be able to get Alec to help too. Her response was something along the lines of hope she gets run over. And mugged. And attacked again. He went back out again for a few hours, but returned home empty handed.

Jace walked into the dining room the next morning to find Clarrisa sitting ideally poking at her food. She pulled a dry erase board with 'Hi' written on it off her lap.

Jace pinched the bridge of his nose. "How the hell did you even get in here!"

Under her 'Hi' she wrote 'I saw you do it. It was a little more difficult though. Did you know the angel takes paper notes? Sit down."

He grabbed her wrist, "Hand me the knife." She slipped the knife delicately from the sleeve of her shirt and laid it gentle on the table. She wrote, 'Good Eye' on her board.

Jace examined it. "This isn't the one from last night."

'Found armory. Very nice, by the way.' She wrote out.

"Fine, whatever, we've established that you're crazy as all hell. Where do insane people like yourself go all night?''

'Just trying to find my old friend, Magnus Bane. You should know him.' She wrote in her small delicate handwriting.


	5. Chapter 4: Commonalities

Chapter 4: Commonalities

'He said he comes over here to do some odd jobs and portal openings and what not. We had a very nice talk. He seems to be doing well for himself.'

Jace sank down into a chair, exasperated. "How did you meet Magnus Bane? You testified that you were locked in a single room with no outside contact besides Sebastian and Valentine."

'You're a little slow. I lied.' She wrote and picked at her food simultaneously.

"How? You were holding the mortal sword."

She shook her head and smirked.

"What was the purpose of lying? How do you benefit from it?" Jace combed his fingers through his hair.

'I lied because I didn't want get Magnus involved, but he said he didn't mind. He said it would entertain him more than parties. Also,,' she pause writing. 'I thought I'd test your reaction first… you seemed nicer than the other shadow hunters.'

'Will you answer a question of mine? Will the clave try to punish me for not telling them this?'

"I don't know maybe. They're strict people. They might put you in a cell for a few days."

'Or forever,' She leaned back into her chair. 'Life's short. Why not poke the bear a little? Let's go talk to my supervisor.'

"Alright, then," He popped up from his chair with mock energy and offered her his hand. She took it with even more enthusiasm giving a spin. Jace shook his head and laughed. He led her by the hand to the main office of the Institute. The room was plain, a desk and two chairs positioned in front of it. Maryse sat sternly with the mortal sword sitting on her desk. "So you've come back, eh? How's your brother?"

Clarissa sat down in one of the chairs and begun writing, 'He's well, generally.' She picked the sword up tenderly in her left hand. It clung to her hands as if it were made out of thorns biting into her skin.

"Where did you go last night?" Maryse said sharply.

'I went to see Magnus Bane. I knew him before I left Idris.'

She narrowed her eyebrows, "What was your relationship with Magnus Bane?"

'He was hired by my father on occasion. He was not aware of my brother's existence or of my father's identity. Whenever my fathered would call on him, I would bring him a note to tell him his job. He would do it and leave.'

"This information will be provided to the clave promptly." She folded her hands, "Was there anywhere else you went?"

'No' She wrote.

"Did you visit Sebastian Morgenstern?"

'No, I don't believe he's stupid enough to visit me, now, doll face .'

Maryse reached across the table and grabbed Clarissa by her hair. She hissed in her ear, "Don't you ever disrespect me again. None of the clave's power will make lenient on you Morgenstern."

She tossed Clarissa back in her chair like a rag doll. Clarissa's head was smashed against the backboard. She gave a small grimace in response. Jace grabbed her by her arm and shuttled her out of the room before more damage could be done. He brought her to a bedroom and sat her own on the bed. "Damn, you're stupid."

Clarissa didn't mind him as her aching head. Jace looked at her sympathetically. He brushed her hair behind her ear. "You shouldn't talk that way with her. She has every right to treat you like she does." He sighed heavily, "You know you're wrong."

He plopped down in a nearby chair. After a moment he started to giggle. "Doll face. I should have thought of that one."


	6. Chapter 5: Love

Chapter 5: Dreams

Clarissa fell asleep fitfully that night. Her thoughts started off on the way Jace had laughed at new name for Maryse. She replayed his small laugh over and over in her head. Every time her heart would beat fast and she would give a smile. She wonder if he liked her. She'd been slightly rude to him. She thought about ways to ask him to walk with her through Central Park. In all the books she'd read, the park was described beautifully. Sebastian, once, told her about an extremely gorgeous place where mundanes didn't go. He said that they sensed the presence of the fae and instinctively avoided.

That led her to thoughts of Sebastian. He was the only kind face she had growing up and, now, people were trying to kill him. She understood that what he has done is terrible and that the things he would do as he became more powerful would be even worse. She had no doubt in her mind that he would become more powerful. She knew he wouldn't stop until he'd reach his goal, whatever it was. She felt so sad thinking about him. She remembered when he'd killed the pet hawk Valentine had given him. That was the first time she realized there was something wrong with him. He'd graduated from birds to people, now. She wondered if she'd ever have her brother back. She recalled the way he was all his life and wondered if she even wanted him back. He'd always been demented. She wondered if she'd end up just like him.

These thoughts carried her off to sleep and leaded her into her dream. She was lying peacefully on the floor of a room she'd never seen before. She moved her hands in front of her eyes to block the stream of sunlight pouring in through the windows. She heard her brothers voice whispering her name and telling her that she needed to get up. She sat up slowly and realized to her left was a door. Standing next in the door frame was her brother. Behind him was a void of pure white. He stepped in and closed the door behind him.

"Hello, sister." he said quietly. He moved to sit next to her on the floor. He hugged her and held her there until he could force himself to let her go. " How are you?"

"I'm okay, brother." She voice sounded so strange to her. It had been years since she heard it. She wondered if it was really hers or a voice her brother had created for her.

Sebastian jumped up, pulling Clarissa with him. He yelled, "I told you I could make it work!" He laughed at his own cleverness. " I said I'd let you talk again and I DID!"

His high of jubilance faded immediately when he saw the look on his sisters face, "Why won't you look at me? Look what I've done for you. Look at this room. It's a haven for us. We can't be tracked here. Soon I'll make it into our own palace. Doesn't that make you happy?

She couldn't bring herself to look into his black eyes. She knew the things he gave her came with a price. She knew someone bought her voice. Someone bought it with their pain and anguish. Why does everything have to have a price?

She rested her head against his chest. "The shadow hunter talk about you. They talk about all the terrible things you've done."

"Don't worry about that, now. I'll explain myself to you soon enough. I have a favor to ask of you first. Watch this."

Sebastian took her hands and held them palms up in front of her. A small, electricity like spark floated up from her skin and came to a rest just above her palm. It tingled like her hands had gone sleep. She closed her eyes lightly, waiting for whatever Sebastian planned for these sparks to do. She heard him giggle at her. The tingle transformed into two different weights.

"Open your eyes. I want you to see your new presents, little sister."

In her left hand was a pad of art paper, and in her left was a pack of pencils.

"You can create wonderful things in this world, Clarissa. This place will be made just as you wish." He stroked her hair. "Do you remember, when you were little and you got mad at Father, and you would scribble those symbols on your coloring books. Do you remember how they just to glow and vibrate with your anger. Do you remember how those scribbles would change emotion based on how you were feeling when you drew them. Would you draw one for me, Clarissa? Draw for me."

She was so confused. She didn't understand why he would want her childish drawings. His grin was so menacing and evil. She stepped away from him and kneeled on the ground. She pressed one of her pencils to the pad of paper and scratched a crude design into it.

Sebastian's grin faded. "Not… No.. Not like that." He knelt down in front of her. "Think of some strong emotion. Something you want. Something you hate. Then draw me a symbol. Don't just move your hand. Make me something."

Clarissa nodded. She thought back to Jace's laugh and his bright smile and the way he took her hand and lifted her from her chair. When she lifted her pencil all the feeling drained from her. She felt so tired she could almost pass out. Sebastian turned the pad towards himself and smiled. "I love you, too"

Clarissa's head spun. Her vision blurred and the room seemed to scene, finally faded, leaving Clarissa alone in her bed in her bedroom.


	7. Chapter 6: Into the Night

Chapter 6 : Into the Night

Clarissa woke inwardly cold. She's expected to see the soft early morning light, bright and optimistic, beaming through her window, but all she got were the shallow afternoon rays. She felt cold someplace deep. She curled herself up tightly, desperately trying to shake away her dreams. She shivered at the thought of her brother's smile when he took that paper. She knew that smile very well. He had plans of her, now. She knew tonight would only be the first of many visits to the dream world Sebastian had created. She whimpered at the thought. Everything there gave off such as strong sense of hatred. She was so glad she had declined to go with her brother. That place would have been hell to live in. At the same time, she loved her brother. He was her only family. The last of her hard, cruel family. She let the thoughts go and tried to ease her mind.

She let her muscles relax with a heavy sigh. 'Nobody should be walking by here, if they let me sleep this long already. I can lay her for a few minutes longer.' She thought peacefully. The "powers that be" decided her to correct her her restful thoughts by having someone knock on her door. She thought angrily. 'But why would I have ever wanted to do that. Peaceful rest is just a ridiculous concept anyway. We should all just boycott it and die of sleep deprivation.'

She proceeded to throw the covers of herself and a walk to open the door, ready to slap Jace for waking her up at this wretched hour. When he opened her door all her sleep deprived hatred faded. He was wearing some of the dark gear, she found looking through the institute's supplied. Jace had his ever so slightly annoying crooked smile, the one he wears when he's got an idea in his head. His mischievous look faded after a second. "Hey, I just wanted to drop by and umm… say something. Not something, I meant I had to tell you where I was going. Well I didn't have to, I wanted to."

Clarissa rolled her eyes at him. Jace said, " Well, I guess I'll tell you where I'm going. Me and Alec are going hunting by central park. We'll be back before morning."

Clarissa beckoned for him to come into her room. Jace stared at her confused, not understanding her gesture. She pulled him by the hand into the room and deposited him on her bed. Jace sat there awkwardly while she got her white board out of a drawer. She wrote, 'What do you hunt?'

Jace stammered, "Um, demons."

She wrote, ' I assumed that. What kind of demons?"

"Any?"

Clarissa giggled. 'You're cute.'

"Am I?" Jace said, regaining his half cocked grin. Clarissa blushed brightly and gave a small smile.

Meanwhile, Alec had been looking for Jace for thirty minutes. He finally decided to look down the corridor that led to the visitors rooms. He couldn't imagine why Jace would need to be in a visitors room, but he wasn't anywhere else. As he was walking he heard laughter coming from one of the rooms. Alec walked closer to it. 'By the Angel,' He thought 'That's Jace.'

Alec walked into the room to find Jace, blushing like a red balloon and grinning like a cheshire cat, sitting on a bed next to Clarissa Morgenstern. The pair both stopped laughing abruptly when he walked in. All three of them stared at each other opened mouthed for at least five seconds before Alec broke "What the sam's hell" . He turned on his house and sprinted from the room all the way to the front room. Jace appeared about a minute later. "Alec."

Alec shook his head , "Let's go."

"Alright" Jace said and with that the pair walked out into the night. They walked the night.

It took them short pace to get city park. They didn't talk on the way there. The hate seemed to emanate off Alec like heat from a fire. Jace didn't mind Alec temper. Alec was always a moody person. Jace always just believed it was Alec's personal quirk. By the time they'd reached their destination it was almost pitch black save for the dim street lights. Jace pulled out a sensor. It flashed intensely red instantly. A sickening scream echoed out of the darkness. Alec fired his bow in the direction of the noise, but the arrow only clanged against a metal street lamp. The creature wailed again, and Alec fired and missed. Jace ran about ten feet from his parabiti.

An inanis demon, a relatively small black creature with harsh protruding limbs and spines, struck his side hard, pushing him to the ground. Jace and the creature thrashed on the pavement. Jace slipped a dagger out of his belt and sank it into the creatures side. The inanis bit Jace's arm and held itself there tightly. Alec saw his opportunity and took a shot, killing the demon. Its blood slashed Jace on his already injured arm.

Alec rushed to Jace's side, took out his stele and began to draw iratzes over Jaces arms. "Bastard, bastard, stupid bastard."

Jace cringed, "What, that was cool!"

Within a few minutes, Jace felt just as he had before being attacked and excitedly jumped up. Alec grabbed him , "You damn lucky bastard. One day you're gonna die doing things like that."

Jace grinned, "AH! So I'm not the bane of your existence anymore."

"What are you talking about?"

"You kind walked in on me and Clarissa. You seemed kind of…. exasperated."

Alec sighed. "Do you really have to flirt with every girl within a mile of you."

"I do not! They flirt with me."

"Clarissa was flirting with you?"

"No, not really. We were just talking."

"She's mute."

"You know what I mean. She's not a terrible person. She's not like her brother."

"I don't know about that. Do you like her?"

"Alec, why don't you just ask me all the philosophical questions. How was the universe created? What is the human condition? Why do we exist, Alec? Can you answer that?"

"It was a simple yes or no question. Why is this such a hard question for you to answer?"

"Nothing's simple, Alec."


End file.
